DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria
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METHODS AND RESOURCES ARTICLE
DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria George N. Ude1 · David O. Igwe1,4 · Chrysten Brown1 · Myron Jackson1 · Alusine Bangura1 · Onyinye Ozokonkwo‑Alor2 · Onyinye C. Ihearahu1 · Obih Chosen2 · Michael Okoro2,3 · Christabel Ene2 · Venatus Chieze2 · Mariam Unachukwu2 · Christie Onyia2 · George Acquaah2 · James Ogbonna2,5 · Aditi Das1 Received: 18 December 2019 / Accepted: 26 May 2020 © The Author(s) 2020
Abstract Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria. Keywords Congeneric · Confamilial · Haplotype · Kimura 2-parameter · Transitional mutation · Phylogenetic diversity
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-020-01155-7) contains supplementary material, which is available to authorized users. * George N. Ude [email protected] 1
Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, MD 20715, USA
2
Godfrey Okoye University, Enugu 01014, Nigeria
3
DNA Learning Center, Cold Spring Harbor, NY 11724, USA
4
Department of Biotechnology, Faculty of Science, Ebonyi State University, Abakalik
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